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NR1H2_HUMAN_213_460

Oxysterols receptor LXR-beta [Nuclear hormone receptor family. NR1 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (NR1H2_HUMAN):R: Transactivation AF-2
required for ligand-dependent transactivation function
mediates interaction with CCAR2 (238, 241, 242, 267, 270, 271, 273, 274, 276, 277, 280, 308, 311, 312, 314, 315, 318, 326, 328, 329, 334, 339, 342:344, 348, 349, 352, 353, 434, 437, 438, 441, 448, 452, 456)
D: NR LBD (238, 241, 242, 267, 270, 271, 273, 274, 276, 277, 280, 308, 311, 312, 314, 315, 318, 326, 328, 329, 334, 339, 342:344, 348, 349, 352, 353, 434, 437, 438, 441, 448, 452, 456)
238, 241, 242, 267, 270, 271, 273, 274, 276, 277, 280, 308, 311, 312, 314, 315, 318, 326, 328, 329, 334, 339, 342:344, 348, 349, 352, 353, 434, 437, 438, 441, 448, 452, 456

Full PDB list

1p8d, 1pq6, 1pq9, 1pqc, 1upv, 1upw, 3kfc, 3l0e, 4dk7, 4dk8, 4nqa, 4rak, 5hjp, 5i4v, 5jy3, 5kya, 5kyj (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
N
2
3
8
S
2
4
1
F
2
4
2
F
2
6
7
F
2
7
0
T
2
7
1
L
2
7
3
A
2
7
4
I
2
7
6
S
2
7
7
E
2
8
0
I
3
0
8
M
3
1
1
L
3
1
2
E
3
1
4
T
3
1
5
R
3
1
8
I
3
2
6
F
3
2
8
L
3
2
9
Y
3
3
4
F
3
3
9
A
3
4
2
G
3
4
3
L
3
4
4
F
3
4
8
I
3
4
9
I
3
5
2
F
3
5
3
H
4
3
4
Q
4
3
7
V
4
3
8
L
4
4
1
L
4
4
8
L
4
5
2
W
4
5
6
[1]1p8d.a co129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pq6.b 96541 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pq6.c none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - -
[1]1pq9.b 44b,bns31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pqc.b 44431 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3kfc.d 61x31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3l0e.a g5836 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4dk7.a 0ks27 . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]4dk8.a 0kt32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4rak.b 65235 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5hjp.b 66835 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5i4v.e 67s33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jy3.b 6ox40 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5kya.e 6y433 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5kyj.e 6y830 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1
N
2
3
8
S
2
4
1
F
2
4
2
F
2
6
7
F
2
7
0
T
2
7
1
L
2
7
3
A
2
7
4
I
2
7
6
S
2
7
7
E
2
8
0
I
3
0
8
M
3
1
1
L
3
1
2
E
3
1
4
T
3
1
5
R
3
1
8
I
3
2
6
F
3
2
8
L
3
2
9
Y
3
3
4
F
3
3
9
A
3
4
2
G
3
4
3
L
3
4
4
F
3
4
8
I
3
4
9
I
3
5
2
F
3
5
3
H
4
3
4
Q
4
3
7
V
4
3
8
L
4
4
1
L
4
4
8
L
4
5
2
W
4
5
6
[1]1p8d.a . . . . . . . . . . . . . . . . . . * . . * . . . . . . . . . . . . . .
[1]1pq6.b . . . * . . . . . . . . . . . . . . * . . . . . . * . . . . . . . . . .
[1]1pq6.c . . . * . . . . . . . . . . . . * . * . . . . . . . . . . . . - - - - -
[1]1pq9.b . . . . . . . . . . . . . . . . . . * . . * . . . . . . . . . . . . . .
[1]1pqc.b . . . * . . . . . . . . . . . . . . * . . * . . . . . . . . . . . . . .
[1]3kfc.d . . . . . . . . . . . . . . . . . . * . . * . . . . . . . . . . . . . .
[1]3l0e.a . . . . . . . . . . . . . . . . . . * . . * . . . . . . . . . . . . . .
[1]4dk7.a . . . . . . . . . . . . * . . . * . * . . * . . . . . . . . . . . . . .
[1]4dk8.a . . . . . . . . . . . . . . . . * . * . . * . . . . . . . . . . . . . .
[1]4rak.b . . . . . . . . . . . . . . . . * . * . . . . . . . . . . . . . . . . *
[1]5hjp.b . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]5i4v.e . . . . . . . . . . . . . . . . . . * . . * . . * . . . . . . . . . . .
[1]5jy3.b . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . *
[1]5kya.e . . . . . . . . . . . . . . . . . . * . . * . . * . . . . . . . . . . .
[1]5kyj.e . . . . . . . . . . . . . . . . . . * . . * . . * . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1p8d.a:co1
1pq6.b:965
1pq6.c is apo
1pq9.b:44b,bns
1pqc.b:444
3kfc.d:61x
3l0e.a:g58
4dk7.a:0ks
4dk8.a:0kt
4rak.b:652
5hjp.b:668
5i4v.e:67s
5jy3.b:6ox
5kya.e:6y4
5kyj.e:6y8
[1] 1p8d.a
0
2.0 - 1.6 1.6 1.0 0.7 0.6 1.2 1.0 1.6 0.5 1.2 0.4 0.5
[1] 1pq6.b 0.9
0
- 1.5 1.5 0.6 1.2 0.1 1.6 1.2 1.1 0.5 1.7 0.3 0.6
[1] 1pq6.c 1.1 1.0
-
2.3 2.1 0.7 1.5 0.1 1.8 0.9 2.2 0.5 1.1 0.6 0.4
[1] 1pq9.b 3.4 3.7 -
0.1
0.2 3.0 4.5 0.3 1.3 4.1 4.2 3.6 4.2 3.9 4.0
[1] 1pqc.b 3.9 3.8 - 0.5
0.1
3.1 4.1 0.6 1.7 3.4 4.5 3.6 3.8 3.4 4.0
[1] 3kfc.d 1.0 1.8 - 2.6 2.2
0
0.8 0.7 1.1 0.7 1.6 0.1 1.2 0 0.2
[1] 3l0e.a 0.9 1.6 - 2.3 2.4 0.1
0.1
0.4 0.9 0.6 2.0 0 1.1 0.1 0.2
[1] 4dk7.a 1.3 2.7 - 2.3 2.0 1.2 1.4
0
1.7 1.8 2.4 0.8 1.7 0.6 1.0
[1] 4dk8.a 2.5 2.8 - 1.6 1.2 1.7 1.5 0.2
0
1.7 2.6 1.9 2.6 1.7 1.3
[1] 4rak.b 1.8 2.0 - 3.2 3.0 0.9 1.3 1.2 1.7
0
1.7 0.3 0.1 0.4 0.4
[1] 5hjp.b 0.6 1.1 - 2.1 2.0 0.2 0.3 0.6 1.0 0.9
0
0.2 1.1 0.1 0.2
[1] 5i4v.e 0.4 1.4 - 2.4 2.2 0.2 0.4 0.5 1.2 0.5 1.4
0
0.8 0 0.2
[1] 5jy3.b 1.8 1.4 - 3.4 3.1 0.8 1.0 1.1 1.5 0 1.7 0.2
0
0.3 0.4
[1] 5kya.e 0.7 1.3 - 2.3 2.2 0.1 0.4 0.3 1.0 0.9 1.2 0.1 1.3
0
0.2
[1] 5kyj.e 1.4 1.9 - 2.7 2.5 0.3 0.5 0.9 1.3 0.7 2.1 0 0.8 0.2
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1p8d.a
1pq6.b
1pq6.c
1pq9.b
1pqc.b
3kfc.d
3l0e.a
4dk7.a
4dk8.a
4rak.b
5hjp.b
5i4v.e
5jy3.b
5kya.e
5kyj.e
[1] 1p8d.a
0
.19 .20 .18 .20 .14 .12 .17 .14 .21 .12 .12 .19 .13 .14
[1] 1pq6.b .19
0
.13 .15 .17 .13 .17 .18 .19 .18 .12 .14 .17 .14 .18
[1] 1pq6.c .20 .13
0
.16 .16 .12 .13 .12 .15 .13 .13 .13 .12 .13 .13
[1] 1pq9.b .18 .15 .16
0
.04 .14 .15 .13 .19 .20 .14 .15 .18 .15 .15
[1] 1pqc.b .20 .17 .16 .04
0
.15 .14 .15 .22 .21 .16 .15 .18 .15 .14
[1] 3kfc.d .14 .13 .12 .14 .15
0
.08 .13 .13 .15 .09 .08 .14 .06 .08
[1] 3l0e.a .12 .17 .13 .15 .14 .08
0
.12 .13 .14 .10 .06 .12 .07 .04
[1] 4dk7.a .17 .18 .12 .13 .15 .13 .12
0
.09 .16 .14 .14 .14 .14 .13
[1] 4dk8.a .14 .19 .15 .19 .22 .13 .13 .09
0
.20 .14 .15 .19 .13 .15
[1] 4rak.b .21 .18 .13 .20 .21 .15 .14 .16 .20
0
.12 .14 .05 .14 .13
[1] 5hjp.b .12 .12 .13 .14 .16 .09 .10 .14 .14 .12
0
.06 .11 .06 .10
[1] 5i4v.e .12 .14 .13 .15 .15 .08 .06 .14 .15 .14 .06
0
.12 .04 .06
[1] 5jy3.b .19 .17 .12 .18 .18 .14 .12 .14 .19 .05 .11 .12
0
.12 .11
[1] 5kya.e .13 .14 .13 .15 .15 .06 .07 .14 .13 .14 .06 .04 .12
0
.06
[1] 5kyj.e .14 .18 .13 .15 .14 .08 .04 .13 .15 .13 .10 .06 .11 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1p8d.a
1pq6.b
1pq6.c
1pq9.b
1pqc.b
3kfc.d
3l0e.a
4dk7.a
4dk8.a
4rak.b
5hjp.b
5i4v.e
5jy3.b
5kya.e
5kyj.e
[1] 1p8d.a
0
1.2 1.3 1.2 1.2 1.3 0.9 0.8 0.8 1.2 0.9 0.9 1.4 0.9 0.9
[1] 1pq6.b 1.2
0
0.6 0.7 0.7 0.6 0.8 1.1 1.2 0.7 0.8 0.7 1.0 0.7 0.7
[1] 1pq6.c 1.3 0.6
0
0.8 0.8 0.8 0.8 1.1 1.2 0.7 0.9 0.8 0.7 0.8 0.8
[1] 1pq9.b 1.2 0.7 0.8
0
0.2 0.8 0.9 1.1 1.2 0.9 0.8 0.8 1.2 0.8 0.8
[1] 1pqc.b 1.2 0.7 0.8 0.2
0
0.8 0.9 1.1 1.2 0.9 0.8 0.9 1.2 0.9 0.8
[1] 3kfc.d 1.3 0.6 0.8 0.8 0.8
0
0.8 1.1 1.2 0.9 0.8 0.7 1.0 0.7 0.7
[1] 3l0e.a 0.9 0.8 0.8 0.9 0.9 0.8
0
0.8 0.8 0.8 0.5 0.4 1.1 0.3 0.4
[1] 4dk7.a 0.8 1.1 1.1 1.1 1.1 1.1 0.8
0
0.4 1.1 0.8 0.9 1.3 0.9 0.9
[1] 4dk8.a 0.8 1.2 1.2 1.2 1.2 1.2 0.8 0.4
0
1.2 0.9 1.0 1.4 0.9 1.0
[1] 4rak.b 1.2 0.7 0.7 0.9 0.9 0.9 0.8 1.1 1.2
0
0.9 0.8 0.7 0.8 0.7
[1] 5hjp.b 0.9 0.8 0.9 0.8 0.8 0.8 0.5 0.8 0.9 0.9
0
0.5 1.1 0.5 0.5
[1] 5i4v.e 0.9 0.7 0.8 0.8 0.9 0.7 0.4 0.9 1.0 0.8 0.5
0
1.0 0.2 0.3
[1] 5jy3.b 1.4 1.0 0.7 1.2 1.2 1.0 1.1 1.3 1.4 0.7 1.1 1.0
0
1.1 1.0
[1] 5kya.e 0.9 0.7 0.8 0.8 0.9 0.7 0.3 0.9 0.9 0.8 0.5 0.2 1.1
0
0.3
[1] 5kyj.e 0.9 0.7 0.8 0.8 0.8 0.7 0.4 0.9 1.0 0.7 0.5 0.3 1.0 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1p8d.a
1pq6.b
1pq6.c
1pq9.b
1pqc.b
3kfc.d
3l0e.a
4dk7.a
4dk8.a
4rak.b
5hjp.b
5i4v.e
5jy3.b
5kya.e
5kyj.e
[1] 1p8d.a
0
2.1 2.0 2.3 2.3 2.3 1.5 1.8 1.4 1.8 1.7 1.5 1.9 1.7 1.5
[1] 1pq6.b 2.1
0
1.4 1.4 1.3 1.4 1.2 1.9 1.8 1.6 1.2 1.4 1.8 1.5 1.4
[1] 1pq6.c 2.0 1.4
0
1.7 1.7 1.5 1.1 1.6 1.6 1.4 1.5 1.2 1.3 1.3 1.2
[1] 1pq9.b 2.3 1.4 1.7
0
0.2 1.2 1.5 1.9 2.0 2.0 1.4 1.8 2.1 1.6 1.8
[1] 1pqc.b 2.3 1.3 1.7 0.2
0
1.2 1.4 1.9 2.0 1.9 1.4 1.8 2.0 1.6 1.8
[1] 3kfc.d 2.3 1.4 1.5 1.2 1.2
0
1.3 1.8 2.0 1.8 1.4 1.6 1.9 1.3 1.6
[1] 3l0e.a 1.5 1.2 1.1 1.5 1.4 1.3
0
1.3 1.2 1.4 0.9 0.7 1.4 0.8 0.8
[1] 4dk7.a 1.8 1.9 1.6 1.9 1.9 1.8 1.3
0
1.0 1.7 1.7 1.4 1.7 1.2 1.4
[1] 4dk8.a 1.4 1.8 1.6 2.0 2.0 2.0 1.2 1.0
0
1.6 1.6 1.2 1.8 1.4 1.2
[1] 4rak.b 1.8 1.6 1.4 2.0 1.9 1.8 1.4 1.7 1.6
0
1.6 1.3 1.2 1.4 1.2
[1] 5hjp.b 1.7 1.2 1.5 1.4 1.4 1.4 0.9 1.7 1.6 1.6
0
1.1 1.7 1.2 1.2
[1] 5i4v.e 1.5 1.4 1.2 1.8 1.8 1.6 0.7 1.4 1.2 1.3 1.1
0
1.3 0.7 0.5
[1] 5jy3.b 1.9 1.8 1.3 2.1 2.0 1.9 1.4 1.7 1.8 1.2 1.7 1.3
0
1.4 1.3
[1] 5kya.e 1.7 1.5 1.3 1.6 1.6 1.3 0.8 1.2 1.4 1.4 1.2 0.7 1.4
0
0.8
[1] 5kyj.e 1.5 1.4 1.2 1.8 1.8 1.6 0.8 1.4 1.2 1.2 1.2 0.5 1.3 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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